Matt Jones

We should have a little example demonstrating how `CassiopeiaTree.reorder_children` can be used to optimize plotting visuals in our plotting tutorial. Mentioned in the discussion around #217.

Per a recent conversation in issue #205, we've determined that our recent software development efforts have outstripped the implementation of the `DistanceSolver` class. Namely, it's become apparent that the inheritance...

Implement utilities from recent [KP-Tracer manuscript](https://www.biorxiv.org/content/10.1101/2021.10.12.464111v1) into the Cassiopeia codebase. Specifically: - Expansion index - Phylogenetic coupling - Phylotime

Make an argument `use_priors` in `CassiopeiaSolvers` that dictates whether or not to use priors during reconstruction of a tree. The current behavior is that if priors exist within a `CassiopeiaTree`,...

Currently we are invoking `copy.deepcopy(self)` when trying to copy a CassiopeiaTree. It would be better to implement a custom version of both `copy` and `deepcopy` for users. See https://docs.python.org/3/library/copy.html ,...